CP3.0.0: ExportToSpreadsheet bug in: Select the measurements to export

cellprofiler
bug
cp3
exporttospreadsheet

#1

Hello,
I recently installed CP3.0.0 both on my Mac and my Linux box (Ubuntu 16.04.3 LTS).
I imported my favorite pipeline from CP2.2.0 but ran into the following problem (on both computers):
When I activate ‘Select the measurements to export’ in the ‘Export to Spreadsheet’ module, it raises an Exception in compile.test_valid saying argument of type ‘ObjectNameSubsciber’ is not iterable

Is it a bug in CP3.0.0 or a shortcoming of the pipeline import from CP2.2.0?

Thanks!
Emmanuel


#2

Hi,

Yes, it is not recommended to import pipeline from CP2.2 to 3.0, quite a few unforeseen bugs may occur.

I personally think that rebuilding the pipeline click-by-click is faster than trying to modifying the pipeline file just to adapt it.

Can you please try.

Bests.


#3

My guess is that it’s a bug, so thanks for reporting it! As @Minh said it’s not hard to rebuild in 3.0, but if we can make drag-and-drop upgrades easier and avoid people having to rebuild pipelines so much the better.

Can you send along your 2.2 pipeline so we can try to validate this and track it down?


#4

Sure. Here it is (attached document)

Sorry for the delay

S2R+Screen_v38.cppipe (25.7 KB)


#5

There is indeed a bug in here, but it’s actually more subtle than just an upgrade issue; ExportToSpreadsheet in 3.0 is not handing correctly cases where in IDSecondary you’re telling it to filter out primary objects whose secondary objects touch the edge of the image. Because of this, even completely remaking the pipeline in 3.0 would not work.

I’ve filed a bug report whose progress you can track here, hopefully we can get it resolved quickly.

Thanks so much for your help!